☰ Navigation Tabs
The structure of the Slackia exigua KARI in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NP3 PDB entry 1NP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 unbuffered 0.2M di-ammonium tartarate and 20% w/v PEG-3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.205 α = 90 b = 118.934 β = 101.17 c = 62.158 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0332 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.39 60.99 92.9 0.039 0.039 12 2.6 137256 137256 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.47 78.9 0.318 0.318 2.2 16986
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1NP3 1.39 60.98 -3 130337 130337 6865 92.86 0.1609 0.1609 0.15954 0.1577 0.1866 0.1852 RANDOM 17.179
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.05 -0.47 -0.31 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 5.836 r_angle_refined_deg 2.744 r_chiral_restr 0.186 r_bond_refined_d 0.029 r_gen_planes_refined 0.018 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 5.836 r_angle_refined_deg 2.744 r_chiral_restr 0.186 r_bond_refined_d 0.029 r_gen_planes_refined 0.018 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5038 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 140
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XSCALE data scaling SCALA data scaling